Pathogenic 12-kb copy-neutral inversion in syndromic intellectual disability identified by high-fidelity long-read sequencing.

Abstract:

:We report monozygotic twin girls with syndromic intellectual disability who underwent exome sequencing but with negative pathogenic variants. To search for variants that are unrecognized by exome sequencing, high-fidelity long-read genome sequencing (HiFi LR-GS) was applied. A 12-kb copy-neutral inversion was precisely identified by HiFi LR-GS after trio-based variant filtering. This inversion directly disrupted two genes, CPNE9 and BRPF1, the latter of which attracted our attention because pathogenic BRPF1 variants have been identified in autosomal dominant intellectual developmental disorder with dysmorphic facies and ptosis (IDDDFP), which later turned out to be clinically found in the twins. Trio-based HiFi LR-GS together with haplotype phasing revealed that the 12-kb inversion occurred de novo on the maternally transmitted chromosome. This study clearly indicates that submicroscopic copy-neutral inversions are important but often uncharacterized culprits in monogenic disorders and that long-read sequencing is highly advantageous for detecting such inversions involved in genetic diseases.

journal_name

Genomics

journal_title

Genomics

authors

Mizuguchi T,Okamoto N,Yanagihara K,Miyatake S,Uchiyama Y,Tsuchida N,Hamanaka K,Fujita A,Miyake N,Matsumoto N

doi

10.1016/j.ygeno.2020.10.038

subject

Has Abstract

pub_date

2020-11-04 00:00:00

eissn

0888-7543

issn

1089-8646

pii

S0888-7543(20)31997-2

pub_type

杂志文章

相关文献

GENOMICS文献大全
  • The gene for the alpha-subunit of retinal rod transducin is on mouse chromosome 9.

    abstract::Mice carrying the autosomal recessive rd gene experience total degeneration of the photoreceptor cells of the retina by 3 to 4 weeks of life. Biochemical studies of the rd retina have demonstrated a lesion in cyclic guanosine monophosphate (cGMP) metabolism due to depressed rod-specific cGMP-phosphodiesterase (cGMP-PD...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1016/0888-7543(89)90303-0

    authors: Danciger M,Kozak CA,Farber DB

    更新日期:1989-02-01 00:00:00

  • Chromosomal assignment of 46 brain cDNAs.

    abstract::Expressed sequence tags (ESTs) have been obtained from several hundred brain cDNAs as an initial effort to characterize expressed brain genes. These ESTs will become tools for human genome mapping and they will also provide candidate causative genes for inherited disorders affecting the central nervous system. We have...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1016/0888-7543(92)90439-y

    authors: Polymeropoulos MH,Xiao H,Glodek A,Gorski M,Adams MD,Moreno RF,Fitzgerald MG,Venter JC,Merril CR

    更新日期:1992-03-01 00:00:00

  • Identification of genes from a 500-kb region at 7q11.23 that is commonly deleted in Williams syndrome patients.

    abstract::Williams syndrome (WS) is a multisystem developmental disorder caused by the deletion of contiguous genes at 7q11.23. Hemizygosity of the elastin (ELN) gene can account for the vascular and connective tissue abnormalities observed in WS patients, but the genes that contribute to features such as infantile hypercalcemi...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1006/geno.1996.0469

    authors: Osborne LR,Martindale D,Scherer SW,Shi XM,Huizenga J,Heng HH,Costa T,Pober B,Lew L,Brinkman J,Rommens J,Koop B,Tsui LC

    更新日期:1996-09-01 00:00:00

  • Identification of non-coding and coding RNAs in porcine endometrium.

    abstract::One of the most critical periods of embryonic loss in pig is day 12 of pregnancy, when implantation begins. Here, we analyzed the gene expression on day 12 of pregnancy and non-pregnancy in the porcine endometrium using RNA sequencing (RNA-seq). 237 mRNAs, 34 lncRNAs and 1 miRNA were significantly differentially expre...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1016/j.ygeno.2016.11.007

    authors: Wang Y,Hu T,Wu L,Liu X,Xue S,Lei M

    更新日期:2017-01-01 00:00:00

  • Repetitive DNA (TGGA)n 5' to the human myelin basic protein gene: a new form of oligonucleotide repetitive sequence showing length polymorphism.

    abstract::DNA 5' to the human myelin basic protein (MBP) gene, mapped to 18q22----qter, is known to manifest multiallelic DNA length variation with heterozygosity of at least 45%. Isolation of genomic DNA containing the MBP gene first exon and its 5' flanking region reveals that this polymorphism arises from a 994-bp region of ...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1016/0888-7543(90)90443-x

    authors: Boylan KB,Ayres TM,Popko B,Takahashi N,Hood LE,Prusiner SB

    更新日期:1990-01-01 00:00:00

  • Localization of the human UBA52 ubiquitin fusion gene to chromosome band 19p13.1-p12.

    abstract::Because of the conservation of the ubiquitin coding sequence and the number of transcriptionally active genes and reverse-transcribed pseudogenes, it has not been possible to use ubiquitin cDNA clones to map the functional ubiquitin genes. The UBB and UBC polyubiquitin genes have previously been mapped by the use of s...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1006/geno.1994.1108

    authors: Webb GC,Baker RT,Coggan M,Board PG

    更新日期:1994-02-01 00:00:00

  • The human transcriptional adaptor genes TADA2L and GCN5L2 colocalize to chromosome 17q12-q21 and display a similar tissue expression pattern.

    abstract::The chromosomal locations and the tissue expression patterns of the human transcriptional adaptors TADA2L and GCN5L2 have been determined. Northern blot analysis across a range of human tissues revealed that both the TADA2L and the GCN5L2 mRNAs are expressed to varying degrees in all tissue types. Furthermore, in most...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1006/geno.1996.4605

    authors: Carter KC,Wang L,Shell BK,Zamir I,Berger SL,Moore PA

    更新日期:1997-03-15 00:00:00

  • Localization of a new type of X-linked liver glycogenosis to the chromosomal region Xp22 containing the liver alpha-subunit of phosphorylase kinase (PHKA2).

    abstract::We describe here a new type of X-linked liver glycogen storage disease. The main symptoms include liver enlargement and growth retardation. The clinical and biochemical abnormalities of this glycogenosis are similar to those of classical X-linked liver glycogenosis due to phosphorylase kinase deficiency (XLG). However...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1006/geno.1994.1322

    authors: Hendrickx J,Coucke P,Hors-Cayla MC,Smit GP,Shin YS,Deutsch J,Smeitink J,Berger R,Lee P,Fernandes J

    更新日期:1994-06-01 00:00:00

  • A class III myosin expressed in the retina is a potential candidate for Bardet-Biedl syndrome.

    abstract::Class III myosins are actin-based motors with amino-terminal kinase domains. Expression of these motors is highly enhanced in retinal photoreceptors. As mutations in the gene encoding NINAC, a Drosophila melanogaster class III myosin, cause retinal degeneration, human homologs of this gene are potential candidates for...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1006/geno.2002.6749

    authors: Dosé AC,Burnside B

    更新日期:2002-05-01 00:00:00

  • Ancient repeated DNA elements and the regulation of the human frataxin promoter.

    abstract::Friedreich ataxia results from frataxin insufficiency caused by repeat expansion in intron 1 of the frataxin gene. Since the coding sequence is unchanged, the potential exists to ameliorate symptoms by increasing frataxin promoter activity. We therefore defined the minimal frataxin promoter in humans. Despite the fact...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1016/j.ygeno.2004.10.013

    authors: Greene E,Entezam A,Kumari D,Usdin K

    更新日期:2005-02-01 00:00:00

  • Isolation of a human chromosome 14-only somatic cell hybrid: analysis using Alu and LINE-based PCR.

    abstract::Interspecific somatic cell hybrids containing single human chromosomes are valuable reagents for localization of cloned genes and DNA fragments to specific chromosomes, for the development of chromosome-specific libraries, and for generation of hybrid cell lines containing subchromosomal regions. A CHO somatic cell hy...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1016/0888-7543(91)90122-u

    authors: Mares A Jr,Ledbetter SA,Ledbetter DH,Roberts R,Hejtmancik JF

    更新日期:1991-09-01 00:00:00

  • A fine integrated map of the SPG4 locus excludes an expanded CAG repeat in chromosome 2p-linked autosomal dominant spastic paraplegia.

    abstract::Autosomal dominant hereditary spastic paraplegia (AD-HSP) is a genetically heterogeneous disorder characterized by progressive spasticity of the lower limbs. A major locus (SPG4) causing AD-HSP in about 40% of the families was mapped to chromosome 2p. The analysis of six SPG4-linked AD-HSP families using the RED proce...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1006/geno.1999.5932

    authors: Hazan J,Davoine CS,Mavel D,Fonknechten N,Paternotte C,Fizames C,Cruaud C,Samson D,Muselet D,Vega-Czarny N,Brice A,Gyapay G,Heilig R,Fontaine B,Weissenbach J

    更新日期:1999-09-15 00:00:00

  • Visual mapping by fiber-FISH.

    abstract::FISH techniques have opened new possibilities for high-resolution genome mapping. Effective utilization of these techniques for the rapid orientation and ordering of adjacent and overlapping probes as well as for the characterization of long-range genomic contigs would facilitate physical mapping and positional clonin...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1006/geno.1995.0005

    authors: Heiskanen M,Hellsten E,Kallioniemi OP,Mäkelä TP,Alitalo K,Peltonen L,Palotie A

    更新日期:1995-11-01 00:00:00

  • Gene expression profiling in livers of mice after acute inhibition of beta-oxidation.

    abstract::Inborn errors of mitochondrial beta-oxidation cause ectopic fat accumulation, particularly in the liver. Fatty liver is associated with insulin resistance and predisposes to hepatic fibrosis. The factors underlying the pathophysiological consequences of hepatic fat accumulation have remained poorly defined. Gene expre...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1016/j.ygeno.2007.08.004

    authors: van der Leij FR,Bloks VW,Grefhorst A,Hoekstra J,Gerding A,Kooi K,Gerbens F,te Meerman G,Kuipers F

    更新日期:2007-12-01 00:00:00

  • Genetic mapping of the mouse neuromuscular mutation kyphoscoliosis.

    abstract::The ky mouse mutant, kyphoscoliosis, exhibits a degenerative muscle disease resulting in chronic deformation of the spinal column. Using an interspecific backcross segregating the ky mutation, we have mapped the ky locus to a small region of mouse chromosome 9. ky is nonrecombinant with the microsatellites D9Mit24 and...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1016/0888-7543(95)80127-8

    authors: Skynner MJ,Gangadharan U,Coulton GR,Mason RM,Nikitopoulou A,Brown SD,Blanco G

    更新日期:1995-01-01 00:00:00

  • Identification of mesoderm development (mesd) candidate genes by comparative mapping and genome sequence analysis.

    abstract::The proximal albino deletions identify several functional regions on mouse Chromosome 7 critical for differentiation of mesoderm (mesd), development of the hypothalamus neuroendocrine lineage (nelg), and function of the liver (hsdr1). Using comparative mapping and genomic sequence analysis, we have identified four nov...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1006/geno.2000.6466

    authors: Wines ME,Lee L,Katari MS,Zhang L,DeRossi C,Shi Y,Perkins S,Feldman M,McCombie WR,Holdener BC

    更新日期:2001-02-15 00:00:00

  • Significant evidence for linkage of mite-sensitive childhood asthma to chromosome 5q31-q33 near the interleukin 12 B locus by a genome-wide search in Japanese families.

    abstract::Childhood-onset asthma is frequently found in association with atopy. Although asthmatic children may develop IgE antibodies against variety of allergens, asthma is associated primarily with allergy to house-dust mites, molds, or other allergens. In this study, we conducted a genome-wide linkage search in 47 Japanese ...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1006/geno.2000.6201

    authors: Yokouchi Y,Nukaga Y,Shibasaki M,Noguchi E,Kimura K,Ito S,Nishihara M,Yamakawa-Kobayashi K,Takeda K,Imoto N,Ichikawa K,Matsui A,Hamaguchi H,Arinami T

    更新日期:2000-06-01 00:00:00

  • Regional localization of human chromosome 15 loci.

    abstract::One hundred forty-nine chromosome 15 loci were mapped by PCR with respect to chromosome breakpoints in three somatic cell hybrids retaining total or part of chromosome 15 and to a 10-Mb YAC contig. This chromosome was subdivided into 5 regions, yielding an average resolution of more than 1 sequence tagged site per meg...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1006/geno.1994.1550

    authors: Richard I,Broux O,Chiannilkulchai N,Fougerousse F,Allamand V,Bourg N,Brenguier L,Devaud C,Pasturaud P,Roudaut C

    更新日期:1994-10-01 00:00:00

  • Deletion mapping of the medulloblastoma locus on chromosome 17p.

    abstract::Isochromosome 17q has previously been observed consistently in cytogenetic studies of medulloblastoma, the most common posterior fossa neoplasm in children. We performed a restriction fragment length polymorphism (RFLP) investigation of medulloblastoma which showed a loss of chromosome 17p sequences in 45% of these tu...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1016/0888-7543(90)90283-z

    authors: Cogen PH,Daneshvar L,Metzger AK,Edwards MS

    更新日期:1990-10-01 00:00:00

  • The genetic equidistance phenomenon at the proteomic level.

    abstract::The field of molecular evolution started with the alignment of a few protein sequences in the early 1960s. Among the first results found, the genetic equidistance result has turned out to be the most unexpected. It directly inspired the ad hoc universal molecular clock hypothesis that in turn inspired the neutral theo...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1016/j.ygeno.2016.03.002

    authors: Luo D,Huang S

    更新日期:2016-07-01 00:00:00

  • Human 4-hydroxyphenylpyruvate dioxygenase gene (HPD).

    abstract::Overlapping DNA fragments spanning approximately 21 kb of genomic DNA and encompassing the human 4-hydroxyphenylpyruvate dioxygenase gene (HPD) have been cloned by screening a human leukocyte genomic library and by PCR amplification of human fibroblastic DNA. A continuous gene sequence of 20,890 nucleotides was establ...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1006/geno.1997.4887

    authors: Rüetschi U,Rymo L,Lindstedt S

    更新日期:1997-09-15 00:00:00

  • Genomic structure of the EWS gene and its relationship to EWSR1, a site of tumor-associated chromosome translocation.

    abstract::The EWS gene has been identified based on its location at the chromosome 22 breakpoint of the t(11;22)(q24;q12) translocation that characterizes Ewing sarcoma and related neuroectodermal tumors. The EWS gene spans about 40 kb of DNA and is encoded by 17 exons. The nucleotide sequence of the exons is identical to that ...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1016/s0888-7543(05)80363-5

    authors: Plougastel B,Zucman J,Peter M,Thomas G,Delattre O

    更新日期:1993-12-01 00:00:00

  • Functional characterization of the human PAX3 gene regulatory region.

    abstract::Spatiotemporal expression of the PAX3 gene is tightly regulated during development. We have isolated and sequenced the 5'-flanking regulatory region of human PAX3. Primer extension and ribonuclease protection mapping revealed that transcription is initiated from a single start site downstream of a TATA-like motif in h...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1006/geno.1998.5711

    authors: Okladnova O,Syagailo YV,Tranitz M,Riederer P,Stöber G,Mössner R,Lesch KP

    更新日期:1999-04-01 00:00:00

  • Expression and chromosomal localization of the human alpha 4/IGBP1 gene, the structure of which is closely related to the yeast TAP42 protein of the rapamycin-sensitive signal transduction pathway.

    abstract::To study the function of the B cell signal transduction molecule alpha 4 (IGBP1), we isolated a human alpha 4 (IGBP1) gene that has sequence similarity to the yeast protein (TAP42) involved in the rapamycin-sensitive signal transduction pathway. The human alpha 4 has sequence identities with murine alpha 4 of 83.4% nu...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1006/geno.1997.5048

    authors: Onda M,Inui S,Maeda K,Suzuki M,Takahashi E,Sakaguchi N

    更新日期:1997-12-15 00:00:00

  • Regional assignment and expression analysis of 29 expressed sequence tags mapped to chromosome 3.

    abstract::Of 311 expressed sequenced tags (ESTs) mapped to single human chromosomes by analysis of a monochromosome somatic cell hybrid panel, 29 were localized to chromosome 3. Analysis of somatic cell hybrid lines containing different regions of chromosome 3 has enabled the regional assignment of these 29 ESTs to 13 of 23 int...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1006/geno.1998.5484

    authors: Jones MH,Tirosvoutis KN,Bowgen C,Davey P,Moore S,Naylor S,Affara NA

    更新日期:1998-11-01 00:00:00

  • Identification of INSL5, a new member of the insulin superfamily.

    abstract::A new member of the insulin gene superfamily (INSL5) was identified by searching EST databases for the presence of the conserved insulin B-chain cysteine motif. Human and murine INSL5 are both polypeptides of 135 amino acids, matching the classical signature of the insulin superfamily. Through the B- and A-chain regio...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1006/geno.1999.5899

    authors: Conklin D,Lofton-Day CE,Haldeman BA,Ching A,Whitmore TE,Lok S,Jaspers S

    更新日期:1999-08-15 00:00:00

  • Cloning of human chromosome 17-specific cDNAs using representational difference analysis and human-mouse hybrid cells.

    abstract::We employed cDNA representational difference analysis (RDA) with human-mouse somatic hybrid cells containing human chromosome 17 and obtained several cDNA clones specific for this chromosome. A cDNA library from PHA-stimulated T cells was screened with unknown cDNA clones obtained by RDA as probes. Subsequently, 1 com...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1006/geno.1997.4729

    authors: Tajima Y,Tashiro K,Camerini D

    更新日期:1997-06-01 00:00:00

  • Reciprocal chromosome painting reveals detailed regions of conserved synteny between the karyotypes of the domestic dog (Canis familiaris) and human.

    abstract::The domestic dog is increasingly being recognized as a useful model for human disease. The aim of this study was to conduct the first detailed whole-genome comparison of human and dog using bidirectional heterologous chromosome painting (reciprocal Zoo-FISH) analysis. We used whole-chromosome paint probes produced fro...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1006/geno.1999.5947

    authors: Breen M,Thomas R,Binns MM,Carter NP,Langford CF

    更新日期:1999-10-15 00:00:00

  • Uroporphyrinogen-III synthase: molecular cloning, nucleotide sequence, expression of a mouse full-length cDNA, and its localization on mouse chromosome 7.

    abstract::Uroporphyrinogen-III synthase (URO-S; EC 4.2.1.75), the fourth enzyme in the heme biosynthetic pathway, is responsible for the conversion of hydroxymethylbilane to the cyclic tetrapyrrole, uroporphyrinogen III. The deficient activity of URO-S is the enzymatic defect in congenital erythropoietic porphyria (CEP), an aut...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1016/0888-7543(95)80175-l

    authors: Xu W,Kozak CA,Desnick RJ

    更新日期:1995-04-10 00:00:00

  • A single segment substitution line population for identifying traits relevant to drought tolerance and avoidance.

    abstract::A population of chromosome segment substitution lines was developed using KDML105 as the recurrent parent and one of DH212 (IR68586-F2-CA-143) or DH103 (IR68586-F2-CA-31) as the donor parent. The donor parents are part of a doubled haploid population from a cross between CT9993, an upland japonica accession, and IR622...

    journal_title:Genomics

    pub_type: 杂志文章,评审

    doi:10.1016/j.ygeno.2019.10.001

    authors: Shearman JR

    更新日期:2019-10-31 00:00:00